The mamewah.ini isn't finding your new layout so it defaults out to the standard one.
I have this:
mamewah.ini =
layout jking_cabthen I created a
jking_cab folder
saved a layout as
layout.lay in that folder
background image is named
main.bmpFor my VirtuaNES layout, I created a file
virtuanes-main.lay within the jking_cab folder. Now it switches with the different emulators. It has a seperate background image
virtuanes-main.bmpIn my case, the layout.lay and main.bmp is the default setup for the jking_cab theme. Until I create emulator-main.lay and a corresponding emulator-main.bmp, newly added emulators will use that default setup.
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I haven't sorted any ROMS yet, I have an idea I'm going to try...

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Snapshots have to have the same file name as the ROM they represent. I'd guess since you're seeing some of them that it's a naming issue. ie:
"abcd_123.zip" needs a corresponding "abcd_123.png"